Highly chromophoric fluorescent-labeled methionyl-initiator tRNAs applicable in living cells

Fluorescent initiator tRNAs (tRNAi) play a crucial role in studying protein synthesis, yet generating highly fluorescent tRNAi complexes remains challenging. We present an optimized strategy to effectively generate highly fluorescent initiator-tRNA complexes in living cells. Our strategy allows the generation of Fluo-Met-tRNAiMet complexes. These complexes can have highly chromogenic N-terminal labeling. For generating such complexes, we use either purified fluorescent methionine (PFM) or non-purified fluorescently labeled methionine (NPFM). Furthermore, PFM promotes the active generation of endogenous tRNAi in cells, leading to highly efficient Fluo-Met-tRNAiMet complexes. Finally, PFM-tRNAiMet complexes also facilitate the visualization of native fluorescently labeled Tat binding to beads. This demonstrates the potential of our approach to advance precision protein engineering and biotechnology applications.

Regulated Behavior in Living Cells with Highly Aligned Configurations on Nanowrinkled Graphene Oxide Substrates: Deep Learning Based on Interplay of Cellular Contact Guidance

Micro-/nanotopographical cues have emerged as a practical and promising strategy for controlling cell fate and reprogramming, which play a key role as biophysical regulators in diverse cellular processes and behaviors. Extracellular biophysical factors can trigger intracellular physiological signaling via mechanotransduction and promote cellular responses such as cell adhesion, migration, proliferation, gene/protein expression, and differentiation. Here, we engineered a highly ordered nanowrinkled graphene oxide (GO) surface via the mechanical deformation of an ultrathin GO film on an elastomeric substrate to observe specific cellular responses based on surface-mediated topographical cues. The ultrathin GO film on the uniaxially prestrained elastomeric substrate through self-assembly and subsequent compressive force produced GO nanowrinkles with periodic amplitude. To examine the acute cellular behaviors on the GO-based cell interface with nanostructured arrays of wrinkles, we cultured L929 fibroblasts and HT22 hippocampal neuronal cells. As a result, our developed cell-culture substrate obviously provided a directional guidance effect. In addition, based on the observed results, we adapted a deep learning (DL)-based data processing technique to precisely interpret the cell behaviors on the nanowrinkled GO surfaces. According to the learning/transfer learning protocol of the DL network, we detected cell boundaries, elongation, and orientation and quantitatively evaluated cell velocity, traveling distance, displacement, and orientation. The presented experimental results have intriguing implications such that the nanotopographical microenvironment could engineer the living cells' morphological polarization to assemble them into useful tissue chips consisting of multiple cell types.

The Portfolio of Evidence for Lab-To-Clinic Innovative Product Bio-Printed Cartilage with Living Cells

Bio-printed cartilage with living cells is a regenerative cartilage scaffold that has living cells 3D printing out for the treatment of osteoarthritis and other conditions that damage articular cartilage. It is a new type of scaffold that is biocompatible, biomimetic, regenerative, and long term in use. Currently, there is a clinical and market lack of products for the regeneration of therapeutic cartilage, so the need for such scaffolds is necessary. Bio-printed cartilage with living cells from concept to product development and non-clinical and clinical testing to market launch requires evaluation of the scaffold for safety, efficacy, and compliance with specific requirements of the medical directives regulation and combined advanced therapy medicinal products.

Living cellular constructs for keratinized tissue augmentation: A 13-year follow-up from a split-mouth randomized, controlled, clinical trial

BACKGROUND

A 13-year follow-up was conducted of a short-term investigation of the use of living cellular construct (LCC) versus free gingival graft (FGG) for keratinized tissue width (KTW) augmentation in natural dentition, to evaluate the long-term outcomes and assess the changes occurring since the end of the original 6-month study.

METHODS

Twenty-four subjects out of the original 29 enrolled participants were available at the 13-year follow-up. The primary endpoint was the number of sites demonstrating stable clinical outcomes from 6 months to 13 years (defined as KTW gain, stability, or ≤0.5 mm of KTW loss, together with reduction, stability, or increase of probing depth, and recession depth [REC] ≤0.5 mm). Secondary outcomes included the assessment of KTW, attached gingiva width (AGW), REC, clinical attachment level, esthetics, and patient-reported outcomes at the 13-year visit, assessing the changes from baseline to 6 months.

RESULTS

Nine sites per group (42.9%) were found to have maintained stable (≤0.5 mm or improved) clinical outcomes from 6 months to 13 years. No significant differences were observed for the clinical parameters between LCC and FGG from 6 months to 13 years. However, the longitudinal mixed model analysis showed that FGG delivered significantly better clinical outcomes over 13 years (p < 0.01). LCC-treated sites exhibited superior esthetic outcomes compared to FGG-treated sites at 6 months and 13 years (p < 0.01). Patient-evaluated esthetics were significantly higher for LCC over FGG (p < 0.01). Patient overall treatment preference was also in favor of LCC (p < 0.01).

CONCLUSIONS

A similar stability of the treatment outcomes from 6 months to 13 years was found for LCC- and FGG-treated sites, with both approaches shown to be effective in augmenting KTW and AGW. However, superior clinical outcomes were found for FGG over 13 years, while LCC was associated with better esthetics and patient-reported outcomes than FGG.

Mechanism of action and side effects of colchicine based on biomechanical properties of cells

Many diseases are related to changes in the biomechanical properties of cells; their study can provide a theoretical basis for drug screening and can explain the internal working of living cells. In this study, the biomechanical properties of nephrocytes (VERO cells), hepatocytes (HL-7702 cells), and hepatoma cells (SMCC-7721 cells) in culture were detected by atomic force microscopy (AFM) to analyse the side effects of colchicine at different concentrations (0.1 μg/mL (A) and 0.2 μg/mL (B)) at the nanoscale for 2, 4 and 6 h. Compared with the corresponding control cells, the damage to the treated cells increased in a dose-dependent manner. Among normal cells, the injury of nephrocytes (VERO cells) was markedly worse than that of hepatocytes (HL-7702 cells) in both colchicine solutions A and B. Based on the analyses of biomechanical properties, the colchicine solution reduced the rate of division and inhibited metastasis of SMCC-7721 cells. By comparing these two concentrations, we found that the anticancer effect of colchicine solution A was greater than that of solution B. Studying the mechanical properties of biological cells can help understand the mechanism of drug action at the molecular level and provide a theoretical basis for preventing the emergence and diagnosis of diseases at the nanoscale.

Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells

Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.

Size-Controlled DNA Tile Self-Assembly Nanostructures Through Caveolae-Mediated Endocytosis for Signal-Amplified Imaging of MicroRNAs in Living Cells

Signal-amplified imaging of microRNAs (miRNAs) is a promising strategy at the single-cell level because liquid biopsy fails to reflect real-time dynamic miRNA levels. However, the internalization pathways for available conventional vectors predominantly involve endo-lysosomes, showing nonideal cytoplasmic delivery efficiency. In this study, size-controlled 9-tile nanoarrays are designed and constructed by integrating catalytic hairpin assembly (CHA) with DNA tile self-assembly technology to achieve caveolae-mediated endocytosis for the amplified imaging of miRNAs in a complex intracellular environment. Compared with classical CHA, the 9-tile nanoarrays possess high sensitivity and specificity for miRNAs, achieve excellent internalization efficiency by caveolar endocytosis, bypassing lysosomal traps, and exhibit more powerful signal-amplified imaging of intracellular miRNAs. Because of their excellent safety, physiological stability, and highly efficient cytoplasmic delivery, the 9-tile nanoarrays can realize real-time amplified monitoring of miRNAs in various tumor and identical cells of different periods, and imaging effects are consistent with the actual expression levels of miRNAs, ultimately demonstrating their feasibility and capacity. This strategy provides a high-potential delivery pathway for cell imaging and targeted delivery, simultaneously offering a meaningful reference for the application of DNA tile self-assembly technology in relevant fundamental research and medical diagnostics.

Spatiotemporal Monitoring of Subcellular mRNAs In Situ via Polyadenine-Mediated Dual-Color Sticky Flares

Spatiotemporal monitoring of multiple low-abundance messenger RNAs (mRNAs) is vitally important for the diagnosis and pathologic analysis of cancer. However, it remains a clinical challenge to monitor and track multiple mRNAs location simultaneously in situ at subcellular level with high efficiency. Herein, we proposed polyA-mediated dual-color sticky flares for simultaneous imaging of two kinds of intracellular mRNA biomarkers. Two kinds of fluorescent DNA specific for GalNac-T mRNA and c-Myc mRNA were functionalized onto gold nanoparticles (AuNPs) through efficient polyadenine (polyA) attachment. By tuning polyA length, the lateral spacing and densities of DNA on AuNPs could be precisely engineered. Compared to the traditional thio-DNA-modified nanoprobes, the uniformity, detection sensitivity, and response kinetics of sticky flares were greatly improved, which enables live-cell imaging of mRNAs with enhanced efficiency. With a sticky-end design, the fluorescent DNA could dynamically trace mRNAs after binding with target mRNAs, which realized spatiotemporal monitoring of subcellular mRNAs in situ. Compared to one target mRNA imaging mode, the multiple target imaging mode allows more accurate diagnosis of cancer. Furthermore, the proposed polyA-mediated dual-color sticky flares exhibit excellent cell entry efficiency and low cytotoxicity with a low-cost and simple assembling process, which provide a pivotal tool for multiple targets imaging in living cells.

Functionally Collaborative Nanostructure for Direct Monitoring of Neurotransmitter Exocytosis in Living Cells

Neurotransmitter exocytosis of living cells plays a vital role in neuroscience. However, the available amperometric technique with carbon fiber electrodes typically measures exocytotic events from one cell during one procedure, which requires professional operations and takes time to produce statistical results of multiple cells. Here, we develop a functionally collaborative nanostructure to directly measure the neurotransmitter dopamine (DA) exocytosis from living rat pheochromocytoma (PC12) cells. The functionally collaborative nanostructure is constructed of metal-organic framework (MOF)-on-nanowires-on-graphene oxide, which is highly sensitive to DA molecules and enables direct detection of neurotransmitter exocytosis. Using the microsensor, the exocytosis from PC12 cells pretreated with the desired drugs (e.g., anticoronavirus drug, antiflu drug, or anti-inflammatory drug) has been successfully measured. Our achievements demonstrate the feasibility of the functionally collaborative nanostructure in the real-time detection of exocytosis and the potential applicability in the highly efficient assessment of the modulation effects of medications on exocytosis.

Review of Chemical Sensors for Hydrogen Sulfide Detection in Organisms and Living Cells

As the third gasotransmitter, hydrogen sulfide (H₂S) is involved in a variety of physiological and pathological processes wherein abnormal levels of H₂S indicate various diseases. Therefore, an efficient and reliable monitoring of H₂S concentration in organisms and living cells is of great significance. Of diverse detection technologies, electrochemical sensors possess the unique advantages of miniaturization, fast detection, and high sensitivity, while the fluorescent and colorimetric ones exhibit exclusive visualization. All these chemical sensors are expected to be leveraged for H₂S detection in organisms and living cells, thus offering promising options for wearable devices. In this paper, the chemical sensors used to detect H₂S in the last 10 years are reviewed based on the different properties (metal affinity, reducibility, and nucleophilicity) of H₂S, simultaneously summarizing the detection materials, methods, linear range, detection limits, selectivity, etc. Meanwhile, the existing problems of such sensors and possible solutions are put forward. This review indicates that these types of chemical sensors competently serve as specific, accurate, highly selective, and sensitive sensor platforms for H₂S detection in organisms and living cells.

Modular Peptide Probe for Protein Analysis

The analysis and regulation of proteins are of great significance for the development of disease diagnosis and treatment. However, complicated analytical environment and complex protein structure severely limit the accuracy of their analysis results. Nowadays, ascribing to the editability and bioactivity of peptides, peptide-based probes could meet the requirements of good selectivity and high affinity to overcome the challenges. In this review, we summarize the advances in the use of modular peptide probes for proteins analysis. It focuses on how to design and optimize the structure of probes, as well as their performance. Then, the strategies and application to improve the analysis result of modular peptide probes are introduced. Finally, we also discuss current challenge and provide some ideas for the future direction for modular peptide probes, hoping to accelerate their clinical transformation.

Terahertz refractive phenotype of living cells

Cellular refractive index is a vital phenotypic parameter for understanding the cell functional activities. So far, there remains technical challenges to obtain refractive index of viable cells at the terahertz frequency in which contains rich information closely related to their physiological status. Here we introduce a label-free optical platform for interrogating cellular phenotypes to measure the refractive index of living cells in near-physiological environments by using terahertz spectroscopy with the combination of cellular encapsulation in a confined solution droplet. The key technical feature with cells encapsulated in aqueous droplets allows for keeping cellular viability while eliminating the strong adsorption of solvent water to terahertz signal. The obtained high signal-to-noise ratio enables to differentiate different cell types (e.g., E. coli, stem cell and cancer cell) and their states under stress conditions. The integrating of terahertz spectroscopy to droplet microfluidic further realizes automated and high-through sample preparation and detection, providing a practical toolkit for potential application in cellular health evaluation and phenotypic drug discovery.

Engineered Living Oriented Electrospun Fibers Regulate Stem Cell Para-Secretion and Differentiation to Promote Spinal Cord Repair

Living biomaterials directly couple with live cells to synthesize functional molecules and respond to dynamic environments, allowing the design, construction and application of next generation composite materials. Improving the coordination and communication between artificial materials and living cells is essential. In this study, collagen self-assembly and micro-sol electrospinning techniques are used to prepare oriented living fiber bundles that can increase the transplantation rate of stem cells in the early stages of inflammation, indirectly enhancing the dynamic regulation of stem cells during inflammation. Additionally, brain-derived neurotrophic factor (BDNF) contained in the fiber can improve the differentiation of bone marrow mesenchymal stem cells (BMSCs) into neurons once the inflammatory storm subsides. The living oriented fiber bundles fully simulate the 3D structure of the central nervous system, activate integrin β1, promote the growth and adhesion of stem cells in the acute stage of inflammation, upregulate anti-inflammatory genes by more than twofold via BMSCs in response to inflammation, and stably release BDNF for up to 4 weeks post-inflammation storm subsidence. Finally, the BDNF induces the differentiation of BMSCs to neurons by enhancing the expression of neural-related genes, which enables the recovery of neurological functions in the later stages of spinal cord injury.

Surface Filtration in Mesoporous Au Films Decorated by Ag Nanoparticles for Solving SERS Sensing Small Molecules in Living Cells

For surface-enhanced Raman spectroscopy (SERS) sensing of small molecules in the presence of living cells, biofouling and blocking of plasmonic centers are key challenges. Here, we have developed a mesoporous Au (AuM) film coated with a Ag nanoparticles (NPs) as a plasmonic sensor (AuM@Ag) to analyze aromatic thiols, which is an example of a small molecule, in the presence of a living cell strain (e.g., MDA-MB-231) as a model living system. The resulting AuM@Ag provides 0.1 nM sensitivity and high reproducibility for thiols sensing. Simultaneously, the AuM@Ag film filters large biomolecules, preventing Raman signals from overlapping produced by large biomolecules. After analysis, the AuM@Ag film undergoes recycling by the full dissolution of the Ag-thiol layer and removal of thiols from AuM. Furthermore, fresh AgNPs are formed for further SERS analysis, which circumvents the Ag oxidation issue. The ease of the AgNPs deposition allows up to 12 cycles of on-demand recycling and sensing even after utilization as a sensor in multicomponent media without enhancement and sensitivity loss. The reported mesoporous film with surface filtering ability and prominent recycling procedure promises to offer a new strategy for the detection of various small molecules in the presence of living cells.

Measuring Molecular Diffusion in Dynamic Subcellular Nanostructures by Fast Raster Image Correlation Spectroscopy and 3D Orbital Tracking

Here we provide demonstration that fast fluorescence fluctuation spectroscopy is a fast and robust approach to extract information on the dynamics of molecules enclosed within subcellular nanostructures (e.g., organelles or vesicles) which are also moving in the complex cellular environment. In more detail, Raster Image Correlation Spectroscopy (RICS) performed at fast timescales (i.e., microseconds) reveals the fast motion of fluorescently labeled molecules within two exemplary dynamic subcellular nanostructures of biomedical interest, the lysosome and the insulin secretory granule (ISG). The measurement of molecular diffusion is then used to extract information on the average properties of subcellular nanostructures, such as macromolecular crowding or molecular aggregation. Concerning the lysosome, fast RICS on a fluorescent tracer allowed us to quantitatively assess the increase in organelle viscosity in the pathological condition of Krabbe disease. In the case of ISGs, fast RICS on two ISG-specific secreting peptides unveiled their differential aggregation propensity depending on intragranular concentration. Finally, a combination of fast RICS and feedback-based 3D orbital tracking was used to subtract the slow movement of subcellular nanostructures from the fast diffusion of molecules contained within them and independently validate the results. Results presented here not only demonstrate the acquired ability to address the dynamic behavior of molecules in moving, nanoscopic reference systems, but prove the relevance of this approach to advance our knowledge on cell function at the subcellular scale.

A Novel fluorescent probe with large Stokes shift for the detection of viscosity changes and its imaging in living cells

As an important cellular micro environmental parameter, viscosity could reflect the status of living cells. Small molecular fluorescent probe is a vital tool to measure the change of viscosity in living cells. A novel fluorescence probe ZL-1 with a large Stokes shift (in methanol it reached to 153 nm and in glycerol it reached to 125 nm) and excellent sensitivity toward viscosity was developed. The sharp enhancement of the emission intensity for the probe ZL-1 from low viscous methanol to high viscous glycerol indicated the probe ZL-1 could be respond to the viscosity variations. Moreover, the probe ZL-1 has been successfully utilized to detect of viscosity variations in living cells.

Ratiometric fluorimetric and colorimetric probe for sensing and imaging pH changes in living cells

Cell, enzyme and tissue activity in living organisms are closely related to intracellular pH. Detecting the changes of intracellular pH is important to understand the physiological and pathological changes in the process of cell metabolism crucial. A pH probe (HTBI) based on hemicyanine was synthesized. The probe solution displayed marked color change from yellow to amaranth with the pH increase from neutral to basic; simultaneously, the emission spectra showed significant redshift. The probe exhibits a ratiometric fluorescence emission (F_586nm /F_542nm ) characteristic with pK_a 8.82. As expected, HTBI exhibited high sensitivity and selectivity for pH, fine photostability, reversibility and low cytotoxicity. Therefore, it would be a very useful tool for measuring the intracellular pH changes.

Long-Lasting and Responsive DNA/Enzyme-Based Programs in Serum-Supplemented Extracellular Media

DNA molecular programs are emerging as promising pharmaceutical approaches due to their versatility for biomolecular sensing and actuation. However, the implementation of DNA programs has been mainly limited to serum-deprived in vitro assays due to the fast deterioration of the DNA reaction networks by the nucleases present in the serum. Here, we show that DNA/enzyme programs are functional in serum for 24 h but are later disrupted by nucleases that give rise to parasitic amplification. To overcome this, we implement three-letter code networks that suppress autocatalytic parasites while still conserving the functionality of DNA/enzyme programs for at least 3 days in the presence of 10% serum. In addition, we define a new buffer that further increases the biocompatibility and conserves responsiveness to changes in molecular composition across time. Finally, we demonstrate how serum-supplemented extracellular DNA molecular programs remain responsive to molecular inputs in the presence of living cells, having responses 6-fold faster than the cellular division rate, and are sustainable for at least three cellular divisions. This demonstrates the possibility of implementing in situ biomolecular characterization tools for serum-demanding in vitro models. We foresee that the coupling of chemical reactivity to our DNA programs by aptamers or oligonucleotide conjugations will allow the implementation of extracellular synthetic biology tools, which will offer new biomolecular pharmaceutical approaches and the emergence of complex and autonomous in vitro models.

Random Lasing from Label-Free Living Cells for Rapid Cytometry of Apoptosis

A random laser carrying the scattering information on a biological host is a promising tool for the characterization of biophysical properties. In this work, random lasing from label-free living cells is proposed to achieve rapid cytometry of apoptosis. Random lasing is achieved by adding biocompatible gain medium to a confocal dish containing cells under optically pumped conditions. The random lasing characteristics are distinct at different stages of cell apoptosis after drug treatment. By analyzing the power Fourier transform results of the random lasing spectra, the percentage of apoptotic cells could be distinguished within two seconds, which is more than an order of magnitude faster than traditional flow cytometry. These results provide a label-free approach for rapid cytometry of apoptosis, which is advantageous for further research of random lasers in the biological field.

Self-Protected DNAzyme Walker with a Circular Bulging DNA Shield for Amplified Imaging of miRNAs in Living Cells and Mice

Abnormal expression of miRNAs is often detected in various human cancers. DNAzyme machines combined with gold nanoparticles (AuNPs) hold promise for detecting specific miRNAs in living cells but show short circulation time due to the fragility of catalytic core. Using miRNA-21 as the model target, by introducing a circular bulging DNA shield into the middle of the catalytic core, we report herein a self-protected DNAzyme (E) walker capable of fully stepping on the substrate (S)-modified AuNP for imaging intracellular miRNAs. The DNAzyme walker exhibits 5-fold enhanced serum resistance and more than 8-fold enhanced catalytic activity, contributing to the capability to image miRNAs much higher than commercial transfection reagent and well-known FISH technique. Diseased cells can accurately be distinguished from healthy cells. Due to its universality, DNAzyme walker can be extended for imaging other miRNAs only by changing target binding domain, indicating a promising tool for cancer diagnosis and prognosis.

Circular versus linear RNA topology: different modes of RNA-RNA interactions in vitro and in human cells

Circular RNA is progressively reported to occur in various species including mammals where it is thought to be involved in the post-transcriptional regulation of gene expression, partly via interactions with microRNA. Here, we asked whether the circular topology causes functional differences to linear forms when interacting with short RNA strands in vitro and in human cells. Kinetic studies with human bladder cancer-derived synthetic circular RNA versus linear transcripts, respectively, with short oligoribonucleotides showed similar association rates for both topologies. Conversely, a substantial topology-related difference was measured for the activation entropy and the activation enthalpy of RNA–RNA annealing. This finding strongly indicates a significant difference of the mechanism of RNA–RNA interactions. To investigate whether these characteristics of circular RNA are biologically meaningful we performed transient transfection experiments with a microRNA-regulated expression system for luciferase in bladder cancer-derived cells. We co-transfected linear or circular RNA containing one microRNA binding site for the target-suppressing microRNA mlet7a. Here, the circular isoform showed a strongly increased competition with microRNA function versus linear versions. In summary, this study suggests novel topology-related characteristics of RNA–RNA interactions involving circRNA in vitro and in living cells.

Spatiotemporal Control over Chemical Assembly in Living Cells by Integration of Acid-Catalyzed Hydrolysis and Enzymatic Reactions

Spatiotemporal control of chemical assembly in living cells remains challenging. We have now developed an efficient and general platform to precisely control the formation of assemblies in living cells. We introduced an O-[bis(dimethylamino)phosphono]tyrosine protection strategy in the self-assembly motif as the Trojan horse, whereby the programmed precursors resist hydrolysis by phosphatases on and inside cells because the unmasking of the enzymatic cleavage site occurs selectively in the acidic environment of lysosomes. After demonstrating the multistage self-assembly processes in vitro by liquid chromatography/mass spectrometry (LC-MS), cryogenic electron microscopy (Cryo-EM), and circular dichroism (CD), we investigated the formation of site-specific self-assembly in living cells using confocal laser scanning microscopy (CLSM), LC-MS, and biological electron microscopy (Bio-EM). Controlling chemical assembly in living systems spatiotemporally may have applications in supramolecular chemistry, materials science, synthetic biology, and chemical biology.

New Adapted In Vitro Technology to Evaluate Biofilm Formation and Antibiotic Activity Using Live Imaging under Flow Conditions

The polymicrobial nature of biofilms and bacterial interactions inside chronic wounds are keys for the understanding of bacterial cooperation. The aim of this present study was to develop a technique to study and visualize biofilm in live imaging under flow conditions (Bioflux™ 200, Fluxion Biosciences). The Bioflux^TM system was adapted using an in vitro chronic wound-like medium (CWM) that mimics the environment encountered in ulcers. Two reference strains of Staphylococcus aureus (Newman) and Pseudomonas aeruginosa (PAO1) were injected in the Bioflux^TM during 24 h to 72 h in mono and coculture (ratio 1:1, bacteria added simultaneously) in the CWM vs. a control medium (BHI). The quantification of biofilm formation at each time was evaluated by inverted microscopy. After 72 h, different antibiotics (ceftazidime, imipenem, linezolid, oxacillin and vancomycin) at 1x MIC, 10x MIC and 100x MIC were administrated to the system after an automatic increase of the flow that mimicked a debridement of the wound surface. Biofilm studies highlighted that the two species, alone or associated, constituted a faster and thicker biofilm in the CWM compared to the BHI medium. The effect of antibiotics on mature or “debrided” biofilm indicated that some of the most clinically used antibiotic such as vancomycin or imipenem were not able to disrupt and reduce the biofilm biomass. The use of a life cell imaging with an in vitro CWM represents a promising tool to study bacterial biofilm and investigate microbial cooperation in a chronic wound context.

Raman spectroscopy and silver nanoparticles for efficient detection of membrane proteins in living cells

Molecular fingerprints revealed by Raman techniques show great potential for biomedical applications, like disease diagnostic through Raman detection of tumor markers and other molecules in the cell membrane. However, SERS substrates used in membrane molecule studies produce enhanced Raman spectra of high variability and challenging band assignments that limit their application. In this work, these drawbacks are addressed to detect membrane-associated hemoglobin (Hb_m) in human erythrocytes through Raman spectroscopy. These cells are incubated with silver nanoparticles (AgNPs) in PBS before Raman measurements. Our results showed that AgNPs form large aggregates in PBS that adhered to the erythrocyte membrane, which enhances Raman scattering by molecules around the membrane, like Hb_m. Also, deoxyHb markers may allow Hb_mdetection in Raman spectra of oxygenated erythrocytes (oxyRBCs). Raman spectra of oxyRBCs incubated with AgNPs showed enhanced deoxyHb signals with good spectral reproducibility, supporting the Hb_mdetection through deoxyHb markers. Instead, Raman spectra of oxyRBCs showed oxyHb bands associated with free cytoplasmic hemoglobin. Other factors influencing Raman detection of membrane proteins are discussed, like bothz-position and dimension of the sample volume. The results encourage membrane protein studies in living cells using Raman spectroscopy, leading to the characterization and diagnostic of different pathologies through a non-invasive technique.

Optical section structured illumination-based Förster resonance energy transfer imaging

Förster resonance energy transfer (FRET) microscopy is an important tool suitable for studying molecular interactions in living cells. Optical section structured illumination microscopy (OS-SIM), like confocal microscopy, has about 200 nm spatial resolution. In this report, we performed quantitative 3-cube FRET imaging in OS-SIM mode and widefield microscopy (WF) mode, respectively, for living cells expressing FRET constructs consisting of Cerulean (C, donor) and Venus (V, acceptor). OS-SIM images exhibited higher resolution than WF images. Four spectral crosstalk coefficients measured under OS-SIM mode are consistent with those measured under WF mode. Similarly, the system calibration factors G and k measured under OS-SIM mode were consistent with those measured under WF mode. The measured FRET efficiency (E) values of C32V and C17V as well as C5V constructs, standard FRET plasmids, in living Hela cells were E C 32 V OSF = 0.32 ± 0.02 , E C 17 V OSF = 0.38 ± 0.02 , and E C 5 V OSF = 0.45 ± 0.03 , and the measured acceptor-to-donor concentration ratios ( R c ) were R C 32 V OSF = 1.07 ± 0.03 , R C 17 V OSF = 1.09 ± 0.03 , and R C 5 V OSF = 1.02 ± 0.04 , consistent with the reported values. Collectively, our data demonstrates that OS-SIM can be integrated into FRET microscopy to build an OS-SIM-FRET with confocal microscopy-like resolution.

iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations

Mapping the network of proteins provides a powerful means to investigate the function of disease genes and to unravel the molecular basis of phenotypes. We present an automated informatics-aided and bioluminescence resonance energy transfer-based approach (iBRET) enabling high-confidence detection of protein-protein interactions in living mammalian cells. A screen of the ABCD1 protein, which is affected in X-linked adrenoleukodystrophy (X-ALD), against an organelle library of peroxisomal proteins demonstrated applicability of iBRET for large-scale experiments. We identified novel protein-protein interactions for ABCD1 (with ALDH3A2, DAO, ECI2, FAR1, PEX10, PEX13, PEX5, PXMP2, and PIPOX), mapped its position within the peroxisomal protein-protein interaction network, and determined that pathogenic missense variants in ABCD1 alter the interaction with selected binding partners. These findings provide mechanistic insights into pathophysiology of X-ALD and may foster the identification of new disease modifiers.

Light-Activated and Self-Driven Autonomous DNA Nanomachine Enabling Fluorescence Imaging of MicroRNA in Living Cells with Exceptional Precision and Efficiency

Owing to their favorable design flexibility and eminent signal amplification ability, DNA nanomachine-supported biosensors have provided an attractive avenue for intracellular fluorescence imaging, especially for DNA walkers. However, this promising option not only suffers from poor controllability but also needs to be supplied with additional driving forces on account of the frequent employment of metal ion-dependent DNAzymes. Aiming at overcoming these obstacles, we introduce some fruitful solutions. On one hand, innovative light-activated walking behavior induced by a photocleavage mode is established on the surfaces of gold nanoparticles, and such a photoselective sensing system can be perfectly prevented from pre-activating during the intracellular delivery process and made to achieve target identification only under irradiation using a moderate ultraviolet light source. On the other hand, this light-switchable sensing frame is encapsulated within a dissociable metal-organic framework (ZIF-8) to facilitate endocytosis and ensure sufficient internal cofactors (Zn²⁺) to realize a self-driven pattern in the acidic environment of the cell lysosome. Based on the abovementioned efforts, the newly constructed autonomous three-dimensional DNA walkers present satisfactory sensitivity (a limit of detection of down to 19.4 pM) and specificity (even distinguishing single-base changes) toward a model biomarker (microRNA-21). More importantly, the sensing method allows determination of the variations in targets in living cancer cells with exceptional precision and efficiency, offering a powerful assay platform for intracellular imaging.

3D Flower-like NiCo Layered Double Hydroxides: An Efficient Electrocatalyst for Non-Enzymatic Electrochemical Biosensing of Hydrogen Peroxide in Live Cells and Glucose in Biofluids

Herein, a hierarchical structure of flower-like NiCo layered double hydroxides (NiCo LDH) microspheres composed of three-dimensional (3D) ultrathin nanosheets was successfully synthesized via a facile hydrothermal approach. The formation of NiCo LDH was confirmed by various physicochemical studies, and the NiCo LDH-modified glassy carbon electrode was used as an efficient dual-functional electrocatalyst for non-enzymatic glucose and hydrogen peroxide (H₂O₂) biosensor. The host matrix of hydrotalcite NiCo LDH exhibits the enhanced electrocatalytic sensing performances with a quick response time (<3 s), wide linear range (50 nM-18.95 mM and 20 nM-11.5 mM) and lowest detection limits (S/N = 3) (10.6 and 4.4 nM) toward glucose and H₂O₂, and also it exhibits good stability, selectivity, and reproducibility. In addition, this biosensor was successfully utilized to the real-time detection of endogenous H₂O₂ produced from live cells and glucose in various biological fluids, and demonstrates that the as synthesized NiCo LDH may provide a successful pathway for physiological and clinical pathological diagnosis.

A novel fluorescent probe for rapid detection of sulfur dioxide in living cells

Sulfur dioxide is one of the reactive sulfur species, which has significant physiological functions in cells. Some physiological processes are closely related to SO₂ in organisms, and the high concentration of SO₂ in living cells can cause many diseases. In order to investigate the unique function of SO₂ at the subcellular level, developing a molecular tool which could detect of SO₂ within organelles is imperative. Hence, we developed a cationic dye named HQ-SO₂ as a new fluorescent probe to specifically monitor SO₂ , which was easy to obtain through one-step reaction. It took Michael addition reaction as the mechanism of reaction for detection of SO₂ . In addition, this probe showed a series of highly favorable properties such as rapid response rate, low cytotoxicity, high selectivity, low detection limit, and good photostability, which enabled the probe to track SO₂ in living cells.

Measuring calibration factors by imaging a dish of cells expressing different tandem constructs plasmids

Three-cube Förster resonance energy transfer (FRET) method is the most extensively applied approach for live-cell FRET quantification. Reliable measurements of calibration factors are crucial for quantitative FRET measurement. We here proposed a modified TA-G method (termed as mTA-G) to simultaneously obtain the FRET-sensitized quenching transition factor (G) and extinction coefficients ratio (γ) between donor and acceptor. mTA-G method includes four steps: (1) predetermining the ratio ranges of the sensitized emission of acceptor (F_C ) to the donor excitation and donor channel image (I_DD [(DA])) for all FRET plasmids; (2) culturing the cells which express every FRET plasmid in one dish respectively; (3) distinguishing and marking the cells expressing different FRET plasmids by detecting their F_C /I_DD (DA) values; (4) linearly fitting F_C /I_AA (DA) (acceptor excitation and acceptor channel image) to I_DD (DA)/I_AA (DA) for different kinds of cells. We implemented mTA-G method by imaging tandem constructs cells with different FRET efficiency cultured in one dish on different days, and obtained consistent G and γ values. mTA-G method not only circumvents switchover of different culture dishes but also keep the constant imaging conditions, exhibiting excellent robustness, and thus will expands the biological applications of quantitative FRET analysis in living cells.

Ratiometric Detection of Mercury (II) Ions in Living Cells Using Fluorescent Probe Based on Bis(styryl) Dye and Azadithia-15-Crown-5 Ether Receptor

Bis(styryl) dye 1 bearing N-phenylazadithia-15-crown-5 ether receptor has been evaluated as a ratiometric fluorescent chemosensor for mercury (II) ions in living cells. In aqueous solution, probe 1 selectively responds to the presence of Hg²⁺ via the changes in the emission intensity as well as in the emission band shape, which is a result of formation of the complex with 1:1 metal to ligand ratio (dissociation constant 0.56 ± 0.15 µM). The sensing mechanism is based on the interplay between the RET (resonance energy transfer) and ICT (intramolecular charge transfer) interactions occurring upon the UV/Vis (380 or 405 nm) photoexcitation of both styryl chromophores in probe 1. Bio-imaging studies revealed that the yellow (500-600 nm) to red (600-730 nm) fluorescence intensity ratio decreased from 4.4 ± 0.2 to 1.43 ± 0.10 when cells were exposed to increasing concentration of mercury (II) ions enabling ratiometric quantification of intracellular Hg²⁺ concentration in the 37 nM-1 μM range.

The Molecular and Pathophysiological Functions of Members of the LNX/PDZRN E3 Ubiquitin Ligase Family

The ligand of Numb protein-X (LNX) family, also known as the PDZRN family, is composed of four discrete RING-type E3 ubiquitin ligases (LNX1, LNX2, LNX3, and LNX4), and LNX5 which may not act as an E3 ubiquitin ligase owing to the lack of the RING domain. As the name implies, LNX1 and LNX2 were initially studied for exerting E3 ubiquitin ligase activity on their substrate Numb protein, whose stability was negatively regulated by LNX1 and LNX2 via the ubiquitin-proteasome pathway. LNX proteins may have versatile molecular, cellular, and developmental functions, considering the fact that besides these proteins, none of the E3 ubiquitin ligases have multiple PDZ (PSD95, DLGA, ZO-1) domains, which are regarded as important protein-interacting modules. Thus far, various proteins have been isolated as LNX-interacting proteins. Evidence from studies performed over the last two decades have suggested that members of the LNX family play various pathophysiological roles primarily by modulating the function of substrate proteins involved in several different intracellular or intercellular signaling cascades. As the binding partners of RING-type E3s, a large number of substrates of LNX proteins undergo degradation through ubiquitin-proteasome system (UPS) dependent or lysosomal pathways, potentially altering key signaling pathways. In this review, we highlight recent and relevant findings on the molecular and cellular functions of the members of the LNX family and discuss the role of the erroneous regulation of these proteins in disease progression.

Surface-Enhanced Raman Spectroscopy of Organic Molecules and Living Cells with Gold-Plated Black Silicon

Black silicon (bSi) refers to an etched silicon surface comprising arrays of microcones that effectively suppress reflection from UV to near-infrared (NIR) while simultaneously enhancing the scattering and absorption of light. This makes bSi covered with a nm-thin layer of plasmonic metal, i.e., gold, an attractive substrate material for sensing of bio-macromolecules and living cells using surface-enhanced Raman spectroscopy (SERS). The performed Raman measurements accompanied with finite element numerical simulation and density functional theory analysis revealed that at the 785 nm excitation wavelength, the SERS enhancement factor of the bSi/Au substrate is as high as 10⁸ due to a combination of electromagnetic and chemical mechanisms. This finding makes the SERS-active bSi/Au substrate suitable for detecting trace amounts of organic molecules. We demonstrate the outstanding performance of this substrate by highly sensitive and specific detection of a small organic molecule of 4-mercaptobenzoic acid and living C6 rat glioma cell nucleic acids/proteins/lipids. Specifically, the bSi/Au SERS-active substrate offers a unique opportunity to investigate the living cells' malignant transformation using characteristic protein disulfide Raman bands as a marker. Our findings evidence that bSi/Au provides a pathway to the highly sensitive and selective, scalable, and low-cost substrate for lab-on-a-chip SERS biosensors that can be integrated into silicon-based photonics devices.

Stretchable Electrochemical Biosensing Platform Based on Ni-MOF Composite/Au Nanoparticle-Coated Carbon Nanotubes for Real-Time Monitoring of Dopamine Released from Living Cells

Existing electrochemical biosensing platforms, using traditional rigid and unstretchable electrodes, cannot monitor the biological signaling molecules released by cells in a mechanically deformed state in real time. Here, a stretchable and flexible electrochemical sensor was developed based on nickel metal-organic framework composite/Au nanoparticle-coated carbon nanotubes (Ni-MOF composite/AuNPs/CNTs) for sensitive detection of dopamine (DA) released by C6 living cells in real time. A Ni-MOF composite was obtained by introducing Ni, NiO, and a carbon frame onto the surface of two-dimensional (2D) Ni-MOF nanosheets using an efficient one-step calcination method. The hybrid of Ni-MOF composite/AuNPs/CNTs that deposited on the poly(dimethylsiloxane) (PDMS) film endowed the sensor with excellent electrochemical performance with a wide linear range of 50 nM to 15 μM and a high sensitivity of 1250 mA/(cm² M) and also provided the sensor with desirable stability against mechanical deformation. Furthermore, the stretchable electrode also displayed good cellular compatibility while C6 living cells can be cultured and proliferated on it with strong adhesion. Then, the DA released by C6 living cells with chemical induction in both natural and stretched states was monitored using our stretchable and flexible electrochemical sensor in real time. This indicates that our new design of flexible Ni-MOF composite/AuNPs/CNTs/PDMS (NACP) film electrodes provides more opportunities for the detection of chemical signals released from cells and soft living organisms even under mechanically deformed states.

High-Yield Production of Water-Soluble MoS2 Quantum Dots for Fe3+ Detection and Cell Imaging

Uniform water-soluble MoS2 quantum dots (WS-MSQDs) were synthesized via a sequential combination of sintering/etching/exfoliation method and solvothermal route. The obtained WS-MSQDs with average size of approximately 3.4 nm exhibited sufficient water solubility and remarkable fluorescence properties. The WS-MSQDs were utilized as a probe for detection of Fe3+ ions with high selectivity and specificity. Furthermore, the WS-MSQDs exhibited high fluorescence stability under different conditions. Finally, the WS-MSQDs were successfully applied for the fluorescence imaging of Fe3+ in living cells, which exhibited practical potential for biomedical applications.

Nile-Red-Based Fluorescence Probe for Selective Detection of Biothiols, Computational Study, and Application in Cell Imaging

A new colorimetric and fluorescence probe NRSH based on Nile-red chromophore for the detection of biothiols has been developed, exhibiting high selectivity towards biothiols over other interfering species. NRSH shows a blue shift in absorption peak upon reacting with biothiols, from 587 nm to 567 nm, which induces an obvious color change from blue to pink and exhibits a 35-fold fluorescence enhancement at 645 nm in red emission range. NRSH displays rapid (<1 min) response for H₂S, which is faster than other biothiols (>5 min). The detection limits of probe NRSH towards biothiols are very low (22.05 nM for H₂S, 34.04 nM for Cys, 107.28 nM for GSH and 113.65 nM for Hcy). Furthermore, NRSH is low cytotoxic and can be successfully applied as a bioimaging tool for real-time monitoring biothiols in HeLa cells. In addition, fluorescence mechanism of probe NRSH is further understood by theoretical calculations.

In Vivo Biosynthesis of Inorganic Nanomaterials Using Eukaryotes-A Review

Bionanotechnology, the use of biological resources to produce novel, valuable nanomaterials, has witnessed tremendous developments over the past two decades. This eco-friendly and sustainable approach enables the synthesis of numerous, diverse types of useful nanomaterials for many medical, commercial, and scientific applications. Countless reviews describing the biosynthesis of nanomaterials have been published. However, to the best of our knowledge, no review has been exclusively focused on the in vivo biosynthesis of inorganic nanomaterials. Therefore, the present review is dedicated to filling this gap by describing the many different facets of the in vivo biosynthesis of nanoparticles (NPs) using living eukaryotic cells and organisms-more specifically, live plants and living biomass of several species of microalgae, yeast, fungus, mammalian cells, and animals. It also highlights the strengths and weaknesses of the synthesis methodologies and the NP characteristics, bio-applications, and proposed synthesis mechanisms. This comprehensive review also brings attention to enabling a better understanding between the living organisms themselves and the synthesis conditions that allow their exploitation as nanobiotechnological production platforms as these might serve as a robust resource to boost and expand the bio-production and use of desirable, functional inorganic nanomaterials.

A caged 2-hydroxyethyl luciferin for bioluminescence imaging of nitroxyl in living cells

Nitroxyl (HNO), a one-electron reduction product of nitric oxide, demonstrates distinct biological and pharmacological activities. Here we designed a bioluminescent turn-on probe, HNO-8, that could be used to visualize HNO without the need for excitation light. HNO-8 was prepared by caging 2-hydroxyethyl luciferin with a triphenylphosphine unit, in which 2-hydroxyethyl luciferin as a novel substrate of firefly luciferase was characterized by stronger and more sustained bioluminescent signals than the most popular substrates of d-luciferin and 6'-aminoluciferin. In vitro experiments showed that HNO-8 could selectively respond to HNO generated from Angeli's salt(AS) in the range 1-50 μM, with a limit of detection of 0.196 μM. The probe was successfully applied for visualizing HNO in luciferase-transfected Huh7 cancer cells. We envision that HNO-8 could be used as a powerful bioluminescent sensor for researching HNO biological roles.

DNA-Driven Two-Layer Core-Satellite Gold Nanostructures for Ultrasensitive MicroRNA Detection in Living Cells

It is a significant challenge to achieve controllable self-assembly of superstructures for biological applications in living cells. Here, a two-layer core-satellite assembly is driven by a Y-DNA, which is designed with three nucleotide chains that hybridized through complementary sequences. The two-layer core-satellite nanostructure (C₃₀ S₅ S₁₀ NS) is constructed using 30 nm gold nanoparticles (Au NPs) as the core, 5 nm Au NPs as the first satellite layer, and 10 nm Au NPs as the second satellite layer, resulting in a very strong circular dichroism (CD) and surface-enhanced Raman scattering. After optimization, the yield is up to 85%, and produces a g-factor of 0.16 × 10^-2 . The hybridization of the target microRNA (miRNA) with the molecular probe causes a significant drop in the CD and Raman signals, and this phenomenon is used to detect the miRNA in living cells. The CD signal has a good linear range of 0.011-20.94 amol ng_RNA^-1 and a limit of detection (LOD) of 0.0051 amol ng_RNA^-1 , while Raman signal with the range of 0.052-34.98 amol ng_RNA^-1 and an LOD of 2.81 × 10^-2 amol ng_RNA^-1 . This innovative dual-signal method can be used to quantify biomolecules in living cells, opening the way for ultrasensitive, highly accurate, and reliable diagnoses of clinical diseases.

2D Nanoarchitectonics: Soft Interfacial Media as Playgrounds for Microobjects, Molecular Machines, and Living Cells

Soft and flexible two-dimensional (2D) systems, such as liquid interfaces, would have much more potentials in dynamic regulation on nano-macro connected functions. In this Minireview article, we focus especially on dynamic motional functions at liquid dynamic interfaces as 2D material systems. Several recent examples are selected to be explained for overviewing features and importance of dynamic soft interfaces in a wide range of action systems. The exemplified research systems are mainly classified into three categories: (i) control of microobjects with motional regulations; (ii) control of molecular machines with functions of target discrimination and optical outputs; (iii) control of living cells including molecular machine functions at cell membranes and cell/biomolecular behaviors at liquid interface. Sciences on soft 2D media with motional freedom and their nanoarchitectonics constructions will have increased importance in future technology in addition to popular rigid solid 2D materials.

Modulation of Living Cell Behavior with Ultra-Low Fouling Polymer Brush Interfaces

Ultra-low fouling and functionalizable coatings represent emerging surface platforms for various analytical and biomedical applications such as those involving examination of cellular interactions in their native environments. Ultra-low fouling surface platforms as advanced interfaces enabling modulation of behavior of living cells via tuning surface physicochemical properties are presented and studied. The state-of-art ultra-low fouling surface-grafted polymer brushes of zwitterionic poly(carboxybetaine acrylamide), nonionic poly(N-(2-hydroxypropyl)methacrylamide), and random copolymers of carboxybetaine methacrylamide (CBMAA) and HPMAA [p(CBMAA-co-HPMAA)] with tunable molar contents of CBMAA and HPMAA are employed. Using a model Huh7 cell line, a systematic study of surface wettability, swelling, and charge effects on the cell growth, shape, and cytoskeleton distribution is performed. This study reveals that ultra-low fouling interfaces with a high content of zwitterionic moieties (>65 mol%) modulate cell behavior in a distinctly different way compared to coatings with a high content of nonionic HPMAA. These differences are attributed mostly to the surface hydration capabilities. The results demonstrate a high potential of carboxybetaine-rich ultra-low fouling surfaces with high hydration capabilities and minimum background signal interferences to create next-generation bioresponsive interfaces for advanced studies of living objects.

Monitoring the Kinetics of the Cellular Uptake of a Metal Carbonyl Conjugated with a Lipidic Moiety in Living Cells Using Synchrotron Infrared Spectromicroscopy

Presented here is the exploitation of synchrotron infrared spectromicroscopy to evaluate the feasibility of monitoring the cellular uptake of rhenium-tris-carbonyl-tagged (Re(CO)₃) lipophilic chains in living cells. To this aim, an in-house thermostated microfluidic device was used to limit water absorption while keeping cells alive. Indeed, cells showed a high survival rate in the microfluidic device over the course of the experiment, proving the short-term biocompatibility of the device. We recorded spectra of single, living, fully hydrated breast cancer MDA-MB231 cells and could follow the penetration of the rhenium complexes for up to 2 h. Despite the strong variations observed in the uptake kinetics between individual cells, the Re(CO)₃ complex was traced inside the cells at low concentration and shown to enter them on the hour time scale by active transport.

Quantum Dots for Monitoring Choline Consumption Process of Living Cells via an Electrostatic Force-Mediated Energy Transfer

In this work, a ratiometric nanoprobe CdS/ZnS-FB was designed for H₂O₂ detection based on FRET assay. Furthermore, CdS/ZnS-FB could work for detecting choline (Ch) and acetylcholine (ACh) since H₂O₂ is the enzyme cascade reaction product. Significantly, the Jurkat T's choline consumption could also be quantitatively measured by monitoring FRET ratio (I₅₂₂/I₄₂₆). Thus, the biosensor could be applied as a universal tool for the detection of choline consumption of living cells, which provides a good potential for the applications in detecting chemical transmitter and cancer diagnosis.

An optical and non-invasive method to detect the accumulation of ubiquitin chains

The accumulations of excess amounts of polyubiquitinated proteins are cytotoxic and frequently observed in pathologic tissue from patients of neurodegenerative diseases. Therefore, optical and non-invasive methods to detect the increase of the amounts of polyubiquitinated proteins in living cells is a promising strategy to find out symptoms and environmental cause of neurodegenerative diseases, also for identifying compounds that could inhibit gathering of polyubiquitinated proteins. Therefore, we generated a pair of fluorescent protein [Azamigreen (Azg) and Kusabiraorange (Kuo)] tagged ubiquitin on its N-terminus (Azg-Ub and Kuo-Ub) and developed an Azg/Kuo-based Fluorescence Resonance Energy Transfer (FRET) assay to estimate the amount of polyubiquitin chains in vitro and in vivo. The FRET intensity was attenuated in the presence of ubiquitin-activating enzyme inhibitor, PYR-41, indicating that both fluorescent ubiquitin is incorporated into ubiquitin chains likewise normal ubiquitin. The FRET intensity was enhanced by the addition of the proteasome inhibitor, MG-132, and was reduced in the presence of the autophagy activator Rapamycin, designating that ubiquitin chains with fluorescent ubiquitin act as the degradation signal equally with normal ubiquitin chains. In summary, the above optical methods provide powerful research tools to estimate the amounts of polyubiquitin chains in vitro and in vivo, especially non-invasively in living cells.

Quantifying the inhibitory effect of Bcl-xl on the action of Mff using live-cell fluorescence imaging

Mitochondrial fission regulates mitochondrial function and morphology, and has been linked to apoptosis. The mitochondrial fission factor (Mff), a tail‐anchored membrane protein, induces excessive mitochondrial fission, contributing to mitochondrial dysfunction and apoptosis. Here, we evaluated the inhibitory effect of Bcl‐xl, an antiapoptotic protein, on the action of Mff by using live‐cell fluorescence imaging. Microscopic imaging analysis showed that overexpression of Mff induced mitochondrial fragmentation and apoptosis, which were reversed by coexpression of Bcl‐xl. Microscopic imaging and live‐cell fluorescence resonance energy transfer analysis demonstrated that Bcl‐xl reconstructs the Mff network from punctate distribution of higher‐order oligomers to filamentous distribution of lower‐order oligomers. Live‐cell fluorescence resonance energy transfer two‐hybrid assay showed that Bcl‐xl interacted with Mff to form heterogenous oligomers with 1 : 2 stoichiometry in cytoplasm and 1 : 1 stoichiometry on mitochondria, indicating that two Bcl‐xl molecules primarily interact with four Mff molecules in cytoplasm, but with two Mff molecules on mitochondria.

Mitochondrial fission factor (Mff)‐mediated mitochondrial fission is positively correlated with the self‐oligomerization of Mff. Bcl‐xl directly interacts with Mff to prevent Mff‐mediated mitochondrial fission and apoptosis. Bcl‐xl interacts with Mff to form heterogenous hexamers with 1 : 2 stoichiometry in cytoplasm and heterogenous tetramers with 1 : 1 stoichiometry on the mitochondrial membrane, respectively.

Refractive-Index-Insensitive Nanolaminated SERS Substrates for Label-Free Raman Profiling and Classification of Living Cancer Cells

Surface-enhanced Raman spectroscopy (SERS) has emerged as an ultrasensitive molecular-fingerprint-based technique for label-free biochemical analysis of biological systems. However, for conventional SERS substrates, SERS enhancement factors (EFs) strongly depend on background refractive index (RI), which prevents reliable spatiotemporal SERS analysis of living cells consisting of different extra-/intracellular organelles with a heterogeneous distribution of local RI values between 1.30 and 1.60. Here, we demonstrate that nanolaminated SERS substrates can support uniform arrays of vertically oriented nanogap hot spots with large SERS EFs (>10⁷) insensitive to background RI variations. Experimental and numerical studies reveal that the observed RI-insensitive SERS response is due to the broadband multiresonant optical properties of nanolaminated plasmonic nanostructures. As a proof-of-concept demonstration, we use RI-insensitive nanolaminated SERS substrates to achieve label-free Raman profiling and classification of living cancer cells with a high prediction accuracy of 96%. We envision that RI-insensitive high-performance nanolaminated SERS substrates can potentially enable label-free spatiotemporal biochemical analysis of living biological systems.

Latent Redox Reporter of 4-Methoxyphenol as Electrochemical Signal Proxy for Real-Time Profiling of Endogenous H2O2 in Living Cells

Hydrogen peroxide (H₂O₂) plays a persuasive role in the human cell physiology. Developing an efficient assay platform and a highly sensitive tracking and quantification of H₂O₂ in a physiological system is crucial to understand the neoplastic changes and/or redox homeostasis of cells. In this study, a novel turn-on latent electrochemical redox probe coupled with electrocatalytic signal amplification strategy is proposed. A custom-made readily available turn-on latent electrochemical probe 4-methoxyphenylboronic acid pinacol ester (4-MPBP) have been designed for the selective detection of endogenous H₂O₂ in live cells. The electrochemical probe composed of a latent electrochemical reporter (4-methoxy phenol, 4-MP) bearing a recognition unit (boronic acid pinacol ester) for H₂O₂ sensing. The selective analyte-triggered chemical transformation releases free electrochemical reporter 4-MP. The amount of H₂O₂ was evaluated electrochemically at glassy carbon electrode (GCE) with a broad detection range of 0.5 μM-1 mM. An amplified signal response of released 4-MP to build a highly sensitive assay tool has been achieved via replacing the GCE transducer electrode with polydopamine@carbonnanotube-molebtinumdisulfie hybrid modified GCE as it delivered an exceptional dynamic detection range of 0.01-100 μM. The innovative blend of electrochemical molecular probe strategy, with electrocatalytic signal amplification technique has delivered outstanding assay performance at trace level sensing of H₂O₂. Next, we set up a platform for real-time in vivo monitoring of the endogenously produced H₂O₂ in Caco-2 and MCF-7 cells through spermine-polyamine analogue and phorbol 12-myristate 13-acetate induction in SSAT/PAO gene and protein kinase C, respectively. As expected, the 4-MPBP latent probe coupled with electrocatalytic signal amplification strategy delivered outstanding performance for in situ H₂O₂ release and tracking over time.

Visualizing Proteasome Activity and Intracellular Localization Using Fluorescent Proteins and Activity-Based Probes

The proteasome is a multi-catalytic molecular machine that plays a key role in the degradation of many cytoplasmic and nuclear proteins. The proteasome is essential and proteasome malfunction is associated with various disease pathologies. Proteasome activity depends on its catalytic subunits which are interchangeable and also on the interaction with the associated regulatory cap complexes. Here, we describe and compare various methods that allow the study of proteasome function in living cells. Methods include the use of fluorescently tagged proteasome subunits and the use of activity-based proteasome probes. These probes can be used in both biochemical assays and in microscopy-based experiments. Together with tagged proteasomes, they can be used to study proteasome localization, dynamics, and activity.

Detecting Zn(II) Ions in Live Cells with Near-Infrared Fluorescent Probes

Two near-infrared fluorescent probes (A and B) containing hemicyanine structures appended to dipicolylamine (DPA), and a dipicolylamine derivative where one pyridine was substituted with pyrazine, respectively, were synthesized and tested for the identification of Zn(II) ions in live cells. In both probes, an acetyl group is attached to the phenolic oxygen atom of the hemicyanine platform to decrease the probe fluorescence background. Probe A displays sensitive fluorescence responses and binds preferentially to Zn(II) ions over other metal ions such as Cd2+ ions with a low detection limit of 0.45 nM. In contrast, the emission spectra of probe B is not significantly affected if Zn(II) ions are added. Probe A possesses excellent membrane permeability and low cytotoxicity, allowing for sensitive imaging of both exogenously supplemented Zn(II) ions in live cells, and endogenously releases Zn(II) ions in cells after treatment of 2,2-dithiodipyridine.

Quantitative FRET measurement based on spectral unmixing of donor, acceptor and spontaneous excitation-emission spectra

The spontaneous excitation-emission (ExEm) spectrum is introduced to the quantitative mExEm-spFRET methodology we recently developed as a spectral unmixing component for quantitative fluorescence resonance energy transfer measurement, named as SPEES-FRET method. The spectral fingerprints of both donor and acceptor were measured in HepG2 cells with low autofluorescence separately expressing donor and acceptor, and the spontaneous spectral fingerprint of HEK293 cells with strong autofluoresence was measured from blank cells. SPEES-FRET was performed on improved spectrometer-microscope system to measure the FRET efficiency (E) and concentration ratio (R _C ) of acceptor to donor vales of FRET tandem plasmids in HEK293 cells, and obtained stable and consistent results with the expected values. Moreover, SPEES-FRET always obtained stable results for the bright and dim cells coexpressing Cerulean and Venus or Cyan Fluorescent Protein (CFP)-Bax and Yellow fluorescent protein (YFP)-Bax, and the E values between CFP-Bax and YFP-Bax were 0.02 for healthy cells and 0.14 for the staurosporine (STS)-treated apoptotic cells. Collectively, SPEES-FRET has very strong robustness against cellular autofluorescence, and thus is applicable to quantitative evaluation on the protein-protein interaction in living cells with strong autofluoresence.